In a large skillet, heat the oil. Add the chorizo and stir over moderately low heat, breaking it up, until cooked through, 10 minutes; transfer to slow cooker.
Add the onion to the skillet and cook over medium heat, stirring, until translucent, 2 minutes. Add the garlic and cook for 1 minute; transfer to slow cooker.
Season the pork generously with salt and pepper and place the pork on skillet and sear for 5 minutes on each side to form a nice brown crust; transfer to slow cooker.
In a blender add water, chipotle peppers including adobo sauce, and oregano. Puree until smooth and pour over pork.
Add diced tomatoes including sauce and bay leaves in slow cooker, and cook on low for 6 hours.
Remove the pork and discard the bay leaves and shred the meat.
Warm corn tortillas on a comal (griddle) so they are pliable. Add some shredded pork down the center of the tortillas. Roll the tortillas tightly and then add a toothpick to each to keep them rolled.
In a deep pan or deep fryer heat the oil over high heat until it is very hot. Carefully drop the flautas into the hot oil. Fry just long enough for the tortillas to get crispy and a light golden color. Turn over at least once using tongs and then drain upright on paper towels to allow excess oil to drain.
Garnish flautas with toppings of your choice.